Positron emission tomography (PET) imaging is an important nuclear medicine method used both for assessment of diseases such as cancer and Alzheimer’s Disease in clinical patients and for research into understanding disease processes and developing new therapies. Using PET imaging to study small animal models of human disease allows for non-invasive assessment of disease progression and response to therapy, reducing the effects of variability in the course of a disease across a population of research animals. Due to the small size of the animals being imaged, PET systems designed for small animal imaging require spatial resolution that is significantly better than that required for imaging human subjects, making the design and construction of these PET systems a significant physics and engineering challenge. We are developing compact PET systems for mouse imaging with two system design goals in mind. In the first, we propose to build a small footprint PET system based on dual-ended readout of 2 x 2 x 100 mm3 axially oriented scintillator crystals readout at either end by low-cost position sensitive photomultiplier tubes (PS-PMTs). This system is designed to operate on a laboratory benchtop or within a containment area such as a biosafety cabinet, where there is not space for current generation animal PET systems. The second system we propose to build is an MRI compatible PET system designed to fit within the bore of a 7T animal MRI system, allowing simultaneous PET and MR imaging of the mouse. This system design uses dual-layer scintillator arrays readout by silicon photomultiplier (SiPM) photodetectors. These SiPM detectors have performance comparable to conventional photomultiplier tubes (PMTs) while being a fraction of the size and immune to magnetic fields seen in MRI imaging. The combination of PET and MRI for these animal studies will enable significant new research into animal models of disease, particularly with neurological and cardiac applications.